Agent Uzumaki
by ArrowverseNaruto
Summary: Losing his Mother in Metropolis as collateral damage to a Superman fighting Naruto Uzumaki's family moved to National city where they thought they would be safe until Fort Rozz crashed and an escapee from the Kryptonian jail took the life of his father. Seven years later he's one of the best agents the DEO has and he is back in National City after Kryptonians almost took it over.
1. Prolouge

I Do Not Own Naruto Or Supergirl

* * *

(Prolouge)

"Now, entering National city, all passengers prepare for departure."

Seated in the back corner of the 2:10 train from Metropolis 25-year-old Naruto Uzumaki stared out the tiny corner of his private cabin at the sprawling city coming into view. He had told Director Henshaw booking him a private cabin would just attract attention but like always, no matter how many experienced field agents agreed, orders from the fat cat brass Generals and politicians trumped that.

It was why he had left the DEO in the first place. Too much red tape, too many different agenda's from different people all trying to accomplish their own goals. Nothing could get done with a system like that. But no one listened to the people who were actually out in the field, fighting against super powered aliens to keep the world safe. All they cared about was winning their next medal or moving up in rank and sometimes good agents died so someone in the capital could getter a bigger paycheck. The system was a joke.

 _"And yet here I am."_ He thought deprecatingly. Back to the place, he promised never to return to all because of an old friend who called in a favor.

"I'm too soft." He muttered grabbing the black duffel bag laying under his chair as the train began to slow. Standing up he exited the cabin holding back at sigh when the eyes of the other passengers locked onto him. It didn't come as a surprise to him, compared to their colorful and varied clothing choices his all black long sleeve collared shirt and cargo pants that were tucked into combat boots he didn't blend in at all. Just another fault of the top dogs being stupid. _"Wear your uniform so the driver can I.D you."_

If they had even bothered to open his file they would know the six whisker-like scars on his face would have been easier to I.D him than black clothing.

Slinging the duffel bag over his shoulder he stepped out of the train as the doors slid open just a Supergirl zoomed past faster than the speed of sound creating a sonic boom shattering the glass windows of the train. "There's no place like home."

* * *

(DEO Headquarters)

"Madam President." Director Henshaw nodded to his Commander in Chief. "Are you calling about the unknown alien man Supergirl found. We don't know anything as of yet."

He had only been found last night but that was left unsaid as he tried to piece together why the President would contact him over one alien. She had never contacted him first about the update on an alien that wasn't hostile. Why start now?

President Marston raised her hand cutting Hank off. "Actually Director I'm calling to inform you of the newest agent arriving in National City today."

"I didn't request a-" Hank started to say confused as to why someone was being assigned to his base without his knowing about it.

"Yes, I know Director. But after the Myriad incident, things have changed. An entire city under the control of aliens, Director that can't be swept under the rug. We needed to do something." President Marston looked away from the camera before frowning and turning back to Hank. "I'm sorry Director but something has come up. Your newest agent is one of the best Hank, I had to call in a big favor to get him to come back. Don't waste it."

"Yes, Madam President." Hank saluted as the line to the white house cut off and the monitor went black.

A new agent, and one the President herself had to call a favor in to get.

"Hank," Alex opened the door to the conference room. "Kara just arrived, and so did someone else. I've never seen him before him."

"That was fast," Hank muttered annoyed. He would have liked a little more of a warning before the agent arrived instead of the thirty seconds he got.

Alex frowned. "What was fast? Do we need to get a team together?"

Hank shook his head. He'd deal with the President's lack of courtesy later. "Not, Agent Danvers. He's our newest agent, I was just debriefed by the President herself about him. Let's go meet him."

* * *

"So are you a new recruit?" Kara asked extending a hand to the strange man standing in the middle of the DEO's base. "Don't worry, it can be a little overwhelming at first but you get used to it."

Naruto looked down at the hand then back up at Supergirls smiling face. It was like she didn't even care about what happened earlier. "You flew past a train station on the way here."

"um, yeah." Kara withdrew her hand feeling awkward at the restrained tone the scarred blonde was using. "How'd you know."

"I was on it," Naruto said narrowing his eyes. "You were flying too fast. You need to slow down in populated area's like that."

 _What?_ Kara chuckled nervously looking around for Alex or Hank. What was with this guy? He was still speaking wieldy like he was holding back from yelling at her and she didn't know why. "I'll be sure to remember that." She said sighing in relief as she saw her sister and Hank coming towards them.

"Remeber what?" Hank asked his eyes switching back and forth between Supergirl and his newest agent. "Oh, this wasn't going to end well."

"Our newest recruit was just asking me I needed to slow down in populated area's." Kara leaned forward nudging Naruto's shoulder. "Did I knock you off your feet?"

Naruto ignored the joke. There wasn't anything funny about what happened. "No, you shattered some of the windows. Three people got hit by flying glass."

"People got...I didn't-"

"Know." Naruto finished for her. "I didn't think you would."

"What's that supposed to mean?" Kara demanded indignantly. If she had known people got her she would've gone back to help them. " I didn't mean to hurt anyone."

"But you did, because like your cousin you're careless with you powers." Naruto switched his eyes to Hank leaving Kara to splutter at the slight against her family "Director, Agent-"

"Naruto Uzumaki. It's been a while, didn't think I would see you back here again."

Kara glowered at Naruto as he shook hands with J'onn before the Director led him away. "He doesn't like me." She said looking at her sister. "And that crack about my powers? What was that?"

"He doesn't know you yet. Give it time, I'm sure he'll come around to your Danvers charm." Alex promised patting Kara's arm. "As for your powers...well."

"You agree with him!"

"No, No!" Alex denied immediately not wanting to hurt her sister. "Or maybe."

"Alex!" Kara shout-whispered starting to pace back and forth a few feet. "How could you agree with him?"

She didn't mean to hurt anyone with her powers, she was a hero! Her powers were used for good and she tried to save as many people as possible. How could her own sister, someone she had known for years, someone she grew up with think she would hurt someone?

"I'm not agreeing with him. We don't even know if you actually hurt anyone. Did you?" Alex said getting Kara to calm down as other agents began to look at the commotion. She didn't want to hurt her sister and learning she was injuring people with her powers by accident wasn't going to go over well.

"I...I don't know."

* * *

"So a Martian?" Naruto asked dropping his bag on the table of the armory. "We were friends for years, why didn't you tell me?"

J'onn sighed shifting into his natural form. "I figured with your history with aliens you wouldn't take it very well."

"Yea, well you should have known my problem is with Kryptonians not, Martians," Naruto said unpacking his equipment.

"We have standard issue gear for you." J'onn transformed back into Hank. "I didn't get much of a heads up on your arrival but we will get you outfitted with the standard gear tomorrow. What is that-"

Naruto looked up from the table that was now covered in a variety of knives, one pistol and two cases of bullets that glowed green. "Kryptonite bullets. Higher ups don't usually let me carry them but after the whole Myriad deal I think they're finally getting it in their heads that Kryptonians can't be judged on supermans actions alone."

"That's not going to go over well here," Hank said eyeing the bullets. "Not with Supergirl or the agents she works with."

"The president asked me to come here, Hank. I only agreed to it the stipulation that Nationals city's DEO divisions bias towards Supergirl wouldn't get in my way." Naruto loaded a clip of Kryptonite bullets into his sidearm.  
"That going to be a problem?"

"Not at all."

Nodding Naruto pulled on a shoulder holster placing two extra clips of regular bullets on his right side and his pistol on the left. Hank could be trusted to keep personal feelings out of the mission but he had his doubts about the rest of the agents. _"This city could be no different than Metropolis."_

And that wasn't going to work for him.

* * *

 **Leave a review with what you think and Pairing choice. Kara Or Lena**

 **The idea for this story came to me when I was watching the DC movies, Man Of Steel and Batman V Superman.**


	2. Cadmus

I Do Not Own Naruto Or Supergirl

* * *

"That man is a total Xenophobe Alex!" Kara stormed around in circles through the med-bay at the DEO. "I mean I just started using my powers and I know now that I have to be more careful, but Superman has been around for years! And he won't even come in while Superman is in the city?"

Alex shrugged checking over the unconscious Kryptonian on the bed. "I asked J'onn about it and he said Naruto's reasons were personal. I'd let it go if I were you, Kara."

"Let it-? Let it go?" Kara swiped a hand through the air. "Oh, no. I can deal with him not liking me, but my cousin has done nothing but protect this world for years. He doesn't deserve some bigots hate just because he is different. I'm going to talk to him!"

"Whoa!" Alex grabbed her sister's arm stopping her from leaving. "Kara you don't even know where he lives."

"I can-"

"Use your powers to find him?" Alex said sarcastically. "Yeah, that will show him you're not abusing your powers."

That brought Kara down from her angry rant. Crap, her sister was right. Using her powers to search the city for one guy so she could yell at him wasn't a good use for them. But he just made her so angry. Three days he had been in National City and he had already made half a dozen wise cracks about her powers.

"Kara, you ok?"

"Of course, why wouldn't I be?"

Alex pointed to the door frame crushed between Kara's fingers which she immediately let go of.

"I'm sorry, I didn't..." Kara trailed off as she realized what she was about to say.

"Kara it's not your fault. Sometimes accidents happen."

"Yeah, well with J'onn and Superman arguing I don't have time for accidents." Kara ran a hand through her hair. Between Agent Uzumaki's dislike for aliens and J'onn's dislike for Clark wanting to get rid of Kryptonite her time with her cousin was being seriously ruined with all the fighting.

"Kara, as much fun as this conversation is, don't you have somewhere to be?" Alex tapped the watch on her wrist. "It wouldn't look good for CATCO's newest reporter to be late on her first day."

"Right! I will see you tonight, Veep and Chinese!"

* * *

XxX

(DEO, Later that Day)

"Agent Uzumaki, did you find anything?"

Naruto shook his head glancing away from the maps pulled up on the screen in front of him. "No, the warehouse was empty. Again."

J'onn sighed as another red x popped up on the maps. "Another dead end. This doesn't look good."

"For the DEO or for you?"

"What is that supposed to mean, _agent_?" J'onn asked as Naruto turned back to the screens.

"Nothing just that since Superman showed, you've been under a lot of pressure to hand over our Kryptonite. Just want to make sure you have your priority's straight."

J'onn clenched his jaw. "You should worry more about yourself than me, agent. I understand you have problems with Kryptonians but that can't affect your professional outlook on the job."

"It doesn't."

"Then why have you been working the graveyard shift for since Superman showed up?"

Naruto lips twitched and his hands tightened in the pocket of his field jacket. "Because director, Superman doesn't work for the DEO and so I have no obligation to work with him. Besides I've been working during the day, just not at HQ or did you forget that you gave me the mission to locate the stolen Kryptonite while you were having #Toomuchfun?"

Before J'onn could retort the doors slid open and Naruto saw agent Danvers run in."

"Hank, bring up channel 8. I think I found our stolen Kryptonite."

"Agent Schott!"

"On it," Winn's fingers clicked on his keyboard for all of two seconds and the screens Naruto was looking at changed to show the news footage of the two super's fighting against John Corben 2.0.

Naruto watched as Supergirl got hit with Kryptonite and went down. He heard Agent Danvers and Schott both gasp in horror as Corben stood over the helpless girl of steel ready to finish her until Superman literally body checked him and sent the cyborg flying.

"Agent Schott, can you triangulate where Corben is going to land?" He asked the new technician gaining a glare from Agent Danvers who was obviously more worried about her sister than the ongoing CADMUS mission.

"I can-"

"KARA!" Alex yelled and Naruto grit his teeth as agent Schott attention was dragged away from the mission as well.

Why couldn't anyone stay on mission?

"I'm fine, I'm fine." "Kara stumbled as Clark supported her weight. "I'm just a little dizzy."

Alex took her sister's arm and helped her to the table as Superman turned his attention on J'onn.

"You told me only the DEO had access to kryptonite. So how would you like to explain what just happened out there?" The man of steel demanded stepping towards the director. "A kryptonite-charged cyborg almost killed Kara. Almost killed me. Start talking, J'onn!"

Naruto took a step forward and placed himself between the two aliens his hand resting on the Sig-Sauer he had holstered on his back. "Why don't you take a step back, big guy."

"A shipment went missing four months ago. We've done all we can to find it."

"J'onn." Naruto hissed looking over his shoulder. "That's classified-"

"Four months, ago," Kara asked.

Clark nodded with a sardonic smile. "Went missing?"

"Stolen." Alex stepped away from her sister. "We thought it was an inside job but everyone in the transport came up clean."

"Enough! Agent Danvers, take a walk." Naruto ordered.

"You can't talk to her like that." Kara moved in front of her sister her eyes dropping to Naruto's hand behind his back and used her x-ray vision to check the weapon he was holding and gasped her eyes flicking back to his when she saw the glowing bullets.

"So you have a mole?"

"We don't know that," J'onn said. He wasn't writing any of his men off without proper proof.

"If you'd gotten rid of it when I told you to-"

"We would have been defenseless when Non and Astra launched Myriad." Naruto took a step closer to Superman when the hero moved to go around him. "Or have forgotten that there was a force even the man of steel couldn't defeat?"

Clark set a heavy hand on the human agent's shoulder and smiled when the telltale sound of a gun being drawn from its holster reached his ears. "That's not going to do you much good."

"Oh, I wouldn't say that." Naruto grinned moving to raise the gun.

J'onn was behind him though and stopped his hand from rising. "Not here. Not now."

Naruto was about to yank his arm away when every monitor and TV in the DEO went blank grabbing everyone's attention. "What the-"

"People of National City. The Earth has been stolen from us." A gray featureless face appeared on the screens.

"And the enemy has come in the guise of heroes." A picture of Kara in Supergirl costume walking came next followed by a short clip of Superman floating in the air.

Next was a clip of the top of a metropolis sky scraper exploding.

"They say they come in peace o protect us from ourselves. But how long will it be before these gods decide to rule instead of serve?" The face said before another clip appeared this time of an alien throwing a car in Krypton Park.

"We are the antidote to their poison. We are the scientists who will show them what humans are capable of. Those who have sided with the invaders will not be spared. You cannot stop us. We are everywhere. We are Cadmus."

The video ended with another picture of Superman and the face before each screen went blank.

"Cadmus," Superman said staring at the screen.

Winn nodded. "Announcing themselves to the world."

Naruto tucked his gun back into its holster. _"So they made their move."_

"Declaring open war."

"They want to kill us," Kara said looking at her cousin. "All of us."

"Cadmus has my father. If they turned John Corben into Metallo, what do you think they've done with him?"

Kara hugged her sister to her side. "We'll find him."

"And stop them." Superman agreed.

"How?" Winn asked. Cadmus just had Metallo nearly beat two Supers. How were they going to beat that?

"Metallo isn't just flesh and blood anymore. Cadmus has given him a metal endoskeleton. Traces of the alloy had to end up on my hands when I hit him. I can analyze it at the Fortress of Solitude." Superman said.

J'onn nodded. "Agent Schott, get Non and Astra's anti-kryptonite technology out of storage. See if you can improve upon it for our two friends here. Agent Uzumaki, your contacts?"

"I have a few favors I can call in."

"Good, get to it."

Naruto nodded walking away from the group as Agent Schott began stuttering about making Superman's new suit. "Idiot wouldn't be so happy if he knew what they were really like."

Pulling out his phone as he reached the elevator he typed a quick message to one of his contacts before getting.

 _Anti-K. Be wary._

Shoving his phone back into his pocket he hit the button for the first floor. He would do what needed to be done to save Earth. From both Foreign and Domestic threats.

* * *

 **Sorry to everyone for the long wait!**

 **Leave a review with what you think and your choice for pairing. Any girl in Supergirl, No harem.**


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